# US 2019/0172552 A1 · Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform

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- Number: US 2019/0172552 A1
- Document ID: US20190172552A1
- Status: Published application
- Kind: A1
- Application number: 16/140,469
- Filed: 2018-09-24
- Published: 2019-06-06
- Earliest claimed: 2013-01-17
- Assignees: Edico Genome, Corp.
- Applicants: Edico Genome, Corp.
- Inventors: Pieter van Rooyen; Michael Ruehle; Robert McMillen
- Web page: https://patentgrep.com/patent/US20190172552A1

## CPC

- G16B 50/30: Data warehousing; Computing architectures
- G06F 13/16: for access to memory bus (G06F13/28 takes precedence)
- G06F 13/4068: {Electrical coupling}
- G06F 13/4265: {on a point to point bus (G06F13/4247, G06F13/4282 take precedence)}
- G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B 30/10: Sequence alignment; Homology search
- G16B 30/20: Sequence assembly
- G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- G16B 40/10: Signal processing, e.g. from mass spectrometry [MS] or from PCR
- G16B 50/00: ICT programming tools or database systems specially adapted for bioinformatics
- G16B 50/50: Compression of genetic data
- H03K 19/17736: Structural details of routing resources
- H10D 84/90: Masterslice integrated circuits
- H10D 84/907: {CMOS gate arrays}
- H10D 89/10: Integrated device layouts
- H10W 20/01: {Manufacture or treatment}
- H10W 20/064: {by modifying the conductivity of conductive parts, e.g. by alloying}
- H10W 20/43: Layouts of interconnections
- H10D 84/938: {Implementation of memory functions}
- H10D 84/983: {Levels of metallisation}
- Y02D 10/00: Energy efficient computing, e.g. low power processors, power management or thermal management
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G06F: ELECTRIC DIGITAL DATA PROCESSING (computer systems based on specific computational models G06N)
- H03K: PULSE TECHNIQUE (measuring pulse characteristics G01R; modulating sinusoidal oscillations with pulses H03C; transmission of digital information H04L; discriminator circuits detecting phase difference between two signals by counting or integrating cycles of oscillation H03D3/04; automatic control, starting, synchronisation or stabilisation of generators of electronic oscillations or pulses where the type of generator is irrelevant or unspecified H03L; coding, decoding or code conversion, in general H03M)
- H10D: INORGANIC ELECTRIC SEMICONDUCTOR DEVICES
- H10W: GENERIC PACKAGES, INTERCONNECTIONS, CONNECTORS OR OTHER CONSTRUCTIONAL DETAILS OF DEVICES COVERED BY CLASS H10
- Y02D: CLIMATE CHANGE MITIGATION TECHNOLOGIES IN INFORMATION AND COMMUNICATION TECHNOLOGIES [ICT], I.E. INFORMATION AND COMMUNICATION TECHNOLOGIES AIMING AT THE REDUCTION OF THEIR OWN ENERGY USE

## Abstract

A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

## Claims

### Claim 1

A system for analyzing genetic sequence data, the system comprising:
a memory, the memory comprising one or more genetic reference sequences and an index of the one or more genetic reference sequences;
a structured application specific integrated circuit (ASIC) comprising a plurality of mask-programmed, hardwired digital logic circuits mask-configured as a plurality of processing engines comprising a mapping module and an alignment module, and
a plurality of physical electrical interconnects comprising an input to the structured ASIC, a memory interface for the structured ASIC, and an output from the structured ASIC;
wherein the input to the structured ASIC is connectable to an electronic data source to receive the plurality of reads of genomic data;
wherein the memory interface for the structured ASIC is configured to access the memory;
wherein the mapping module is configured to access the index of the one or more genetic reference sequences from the memory via the memory interface and configured to map a read to one or more segments of the one or more genetic reference sequences based on the index of the one or more genetic reference sequences;
wherein the alignment module is configured to access the one or more genetic reference sequences from the memory via the memory interface to align the read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping module; and
wherein the output from the structured ASIC is configured to communicate result data from the mapping module and/or the alignment module.

### Claim 2 (depends on 1)

The system according to claim 1, wherein the mapping module is configured to access the index of the one or more genetic reference sequences according to at least some of the sequence of nucleotides in a read of the plurality of reads.

### Claim 3 (depends on 1)

The system according to claim 1 wherein the index of the one or more genetic reference sequences further comprises a hash table, and wherein the mapping module is configured to apply a hash function to the at least some of the sequence of nucleotides to access the hash table of the index.

### Claim 4 (depends on 1)

The system according to claim 1 wherein the structured ASIC and the memory are housed on an expansion card.

### Claim 5 (depends on 1)

The system according to claim 1 further comprising a sequencer, the sequencer comprising the electronic data source.

### Claim 6 (depends on 5)

The system according to claim 5 wherein the structured ASIC is physically integrated with the sequencer.

### Claim 7 (depends on 1)

The system according to claim 1 further comprising a cloud computing cluster comprising one or more servers, wherein the structured ASIC is housed in at least one of the one or more servers, the cloud computing cluster further comprising the electronic data source.

### Claim 8

A structured application specific integrated circuit (ASIC) for analyzing genetic sequence data, the structured ASIC comprising:
a plurality of mask-programmed, hardwired digital logic circuits mask configured as a plurality of processing engines comprising a mapping module and an alignment module; and
a plurality of physical electrical interconnects comprising an input to the structured ASIC, a memory interface for the structured ASIC, and an output from the structured ASIC;
wherein the input to the structured ASIC is configured to receive a plurality of reads of genomic data;
wherein the mapping module is configured to access an index of one or more genetic reference sequences via the memory interface and configured to map a read to one or more segments of the one or more genetic reference sequences based on the index of the one or more genetic reference sequences;
wherein the alignment module is configured to access the one or more genetic reference sequences via the memory interface to align the read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping module; and
wherein the output from the structured ASIC is configured to communicate result data from the mapping module and/or the alignment module.

### Claim 9 (depends on 8)

The structured ASIC according to claim 8 wherein the mapping module is configured to access the index of the one or more genetic reference sequences according to at least some of the sequence of nucleotides in a read of the plurality of reads.

### Claim 10 (depends on 8)

The structured ASIC according to claim 8 wherein the index of the one or more genetic reference sequences further comprises a hash table, and wherein the mapping module is configured to apply a hash function to the at least some of the sequence of nucleotides to access the hash table of the index.

### Claim 11

A structured application-specific integrated circuit (ASIC) for analyzing genetic sequence data from an electronic data source that provides digital signals representing a plurality of reads of genomic data, each of the plurality of reads of genomic data comprising a sequence of nucleotides, and using a memory storing one or more genetic reference sequences associated with genomic data and an index of the one or more genetic reference sequences, the structured ASIC comprising:
a master slice that includes a set of digital logic circuits; and one or more configurable metal layers formed on the master slice, each of the one or more configurable metal layers having a set of wired connections, the wired connections of the one or more configurable metal layers being arranged to interconnect a subset of the digital logic circuits to form a set of processing engines, the set of processing engines comprising:
a mapping engine to access the index of the one or more genetic reference sequences from the memory to map the read to one or more segments of the one or more genetic reference sequences based on the index; and an
alignment engine to access the one or more genetic reference sequences from the memory to align the read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping engine.

### Claim 12 (depends on 11)

The structured ASIC in accordance with claim 11, wherein the set of processing engines further comprises a sorting engine to sort each aligned read according to the one or more positions in the one or more genetic reference sequences.

### Claim 13 (depends on 11)

The structured ASIC in accordance with claim 11, wherein a portion of the set of digital logic circuits is hardwired in the master slice as a base calling engine to analyze the genetic sequence data from the electronic data source to determine a most likely nucleotide at each position sequenced by the sequencer, and to estimate a confidence of the most likely nucleotide.

### Claim 14 (depends on 11)

The structured ASIC in accordance with claim 11, wherein a portion of the set of digital logic circuits is hardwired in the master slice as one or more embedded processor cores.

### Claim 15 (depends on 14)

The structured ASIC in accordance with claim 14, wherein one or more processing engines of the set of processing engines are connected to the one or more embedded processor cores via the one or more configurable metal layers formed on the master slice.

### Claim 16 (depends on 11)

The structured ASIC in accordance with claim 11, wherein the set of processing engines further comprises a primary analysis pipeline engine, the primary analysis pipeline engine executing on the genomic data one or more of:
signal processing, image processing, base calling, and base call quality estimation.

### Claim 17

A method of making a structured application-specific integrated circuit (ASIC) for analyzing genetic sequence data, the method comprising:
providing a plurality of photolithographic masks that define a set of digital logic circuits of the structured ASIC;
forming the set of digital logic circuits using the plurality of photolithographic masks to form a first master slice and a second master slice that is equivalent to the first master slice;
providing a first set of configurable metal layer masks that define a first digital logic configuration;
forming a first set of configurable metal layers onto the first master slice using the first set of configurable metal layer masks, the first set of configurable metal layers having a set of wired connections arranged according to the first set of configurable metal layer masks to interconnect a subset of the digital logic circuits of the first master slice according to the first digital logic configuration;
providing a second set of configurable metal layer masks that define a second digital logic configuration;
forming a second set of configurable metal layers onto the second master slice using the second set of configurable metal layer masks, the second set of configurable metal layers having a set of wired connections arranged according to the second set of configurable metal layer masks to interconnect a subset of the digital logic circuits of the second master slice according to the second digital logic configuration;
the first digital logic configuration including an input for connecting to an electronic data source that provides digital signals representing a plurality of reads of genomic data, each of the plurality of reads of genomic data comprising a sequence of nucleotides, the first digital logic configuration further including a memory interface to a memory storing one or more genetic reference sequences associated with genomic data and an index of the one or more genetic reference sequences; and
the first digital logic configuration further including a set of processing engines, the set of processing engines comprising a mapping engine to access the index of the one or more genetic reference sequences from the memory to map the read to one or more segments of the one or more genetic reference sequences based on the index.

### Claim 18

An apparatus for analyzing genetic sequence data, the genetic sequence data comprising one or more genetic reference sequences and one or more reads of genomic data, the apparatus comprising:
a memory comprising one or more genetic reference sequences and an index of the one or more genetic reference sequences;
a structured application specific integrated circuit (ASIC) comprising
a plurality of physical electrical interconnects comprising an input to the structured ASIC configured to receive one or more reads of the genomic sequence data, a memory interface for the structured ASIC, and an output from the structured ASIC;
a plurality of mask-programmed, hardwired digital logic circuits interconnected by the plurality of physical electrical interconnects, the plurality of mask-programmed, hardwired digital logic circuits mask-configured to access, according to at least some of the sequence of nucleotides in at least one read of the one or more reads of genomic data, the index of the one or more genetic reference sequences from the memory via the memory interface,
map the at least one read of the one or more reads of genomic data to one or more segments of the one or more genetic reference sequences based on the index,
access the one or more genetic reference sequences from the memory via the memory interface, and
align the read to one or more positions in the one or more segments of the one or more genetic reference sequences